diff --git a/.gitignore b/.gitignore index 5abb7c2..3a90fff 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,4 @@ openbabel-2.0.2.tar.gz /openbabel-2.3.0b2-20100803-r3942.tar.gz /openbabel-2.3.0.tar.gz +/openbabel-2.3.1.tar.gz diff --git a/openbabel-2.3.0-obenergy-fflist.patch b/openbabel-2.3.0-obenergy-fflist.patch deleted file mode 100644 index 4ee2e05..0000000 --- a/openbabel-2.3.0-obenergy-fflist.patch +++ /dev/null @@ -1,18 +0,0 @@ ---- openbabel-2.3.0_orig/tools/obenergy.cpp 2010-10-10 06:05:20.000000000 +0400 -+++ openbabel-2.3.0/tools/obenergy.cpp 2011-03-19 18:58:18.000000000 +0300 -@@ -40,6 +40,7 @@ - int verbose = 0; - bool hydrogens = false; - string basename, filename = "", option, option2, ff = ""; -+ OBConversion conv; - - if (argc < 2) { - cout << "Usage: obenergy [options] " << endl; -@@ -89,7 +90,6 @@ - } - - // Find Input filetype -- OBConversion conv; - OBFormat *format_in = conv.FormatFromExt(filename.c_str()); - - if (!format_in || !conv.SetInFormat(format_in)) { diff --git a/openbabel-inchi.patch b/openbabel-inchi.patch deleted file mode 100644 index 88d538e..0000000 --- a/openbabel-inchi.patch +++ /dev/null @@ -1,37 +0,0 @@ -diff -up openbabel-2.3.0/cmake/modules/FindInchi.cmake.r openbabel-2.3.0/cmake/modules/FindInchi.cmake ---- openbabel-2.3.0/cmake/modules/FindInchi.cmake.r 2010-10-13 02:37:01.000000000 +0200 -+++ openbabel-2.3.0/cmake/modules/FindInchi.cmake 2010-11-23 01:56:55.081622107 +0100 -@@ -13,7 +13,7 @@ if(INCHI_INCLUDE_DIR AND INCHI_LIBRARY) - # in cache already - set(INCHI_FOUND TRUE) - else() -- find_path(INCHI_INCLUDE_DIR NAMES inchi_api.h) -+ find_path(INCHI_INCLUDE_DIR NAMES inchi_api.h PATHS /usr/include/inchi ) - find_library(INCHI_LIBRARY NAMES inchi Inchi) - include(FindPackageHandleStandardArgs) - find_package_handle_standard_args(INCHI DEFAULT_MSG INCHI_LIBRARY -diff -up openbabel-2.3.0/include/CMakeLists.txt.r openbabel-2.3.0/include/CMakeLists.txt ---- openbabel-2.3.0/include/CMakeLists.txt.r 2010-09-25 17:05:05.000000000 +0200 -+++ openbabel-2.3.0/include/CMakeLists.txt 2010-11-23 01:56:55.082628237 +0100 -@@ -4,7 +4,9 @@ file(GLOB math_headers openbabel/ma - file(GLOB stereo_headers openbabel/stereo/*.h) - file(GLOB depict_headers openbabel/stereo/*.h) - -+if(NOT OPENBABEL_USE_SYSTEM_INCHI) - install(FILES inchi_api.h DESTINATION include/inchi) -+endif(NOT OPENBABEL_USE_SYSTEM_INCHI) - install(FILES chemdrawcdx.h DESTINATION ${OB_INCLUDE_DIRS}/openbabel) - install(FILES ${openbabel_headers} DESTINATION ${OB_INCLUDE_DIRS}/openbabel) - install(FILES ${math_headers} DESTINATION ${OB_INCLUDE_DIRS}/openbabel/math) -diff -up openbabel-2.3.0/scripts/ruby/extconf.rb.r openbabel-2.3.0/scripts/ruby/extconf.rb ---- openbabel-2.3.0/scripts/ruby/extconf.rb.r 2010-10-23 03:54:40.000000000 +0200 -+++ openbabel-2.3.0/scripts/ruby/extconf.rb 2010-11-23 01:56:55.083627521 +0100 -@@ -17,7 +17,7 @@ dir_config('openbabel') - # Find a trivial header in order to add the proper include path - # to the build flags. - here = File.dirname(__FILE__) --find_header('inchi_api.h', here + '/../../include') -+find_header('inchi_api.h', '/usr/include/inchi', '/usr/include', here + '/../../include') - - # Prevent Ruby 1.8.x from trying to compile and link the extension - # using gcc. diff --git a/openbabel-rpm.patch b/openbabel-rpm.patch index 3f7d1a1..7d8e12f 100644 --- a/openbabel-rpm.patch +++ b/openbabel-rpm.patch @@ -1,91 +1,12 @@ -diff -up openbabel-2.3.0/scripts/CMakeLists.txt.r openbabel-2.3.0/scripts/CMakeLists.txt ---- openbabel-2.3.0/scripts/CMakeLists.txt.r 2010-10-25 19:37:42.000000000 +0200 -+++ openbabel-2.3.0/scripts/CMakeLists.txt 2010-11-24 22:53:29.250004683 +0100 -@@ -82,6 +82,7 @@ if (DO_PYTHON_BINDINGS) - COMMAND ${CMAKE_COMMAND} -E copy ob.py ${openbabel_SOURCE_DIR}/scripts/python/openbabel.py - COMMAND ${CMAKE_COMMAND} -E remove ob.py - VERBATIM) -+ add_dependencies(_openbabel openbabel) - - if (PYTHON_PREFIX) - install(CODE "execute_process(COMMAND ${PYTHON_EXECUTABLE} ${openbabel_SOURCE_DIR}/scripts/python/setup.py install --prefix=${PYTHON_PREFIX} WORKING_DIRECTORY ${openbabel_BINARY_DIR}/scripts)") -@@ -89,7 +90,7 @@ if (DO_PYTHON_BINDINGS) - if (${CMAKE_INSTALL_PREFIX} STREQUAL "/usr/local") - install(CODE "execute_process(COMMAND ${PYTHON_EXECUTABLE} ${openbabel_SOURCE_DIR}/scripts/python/setup.py install WORKING_DIRECTORY ${openbabel_BINARY_DIR}/scripts)") - else (${CMAKE_INSTALL_PREFIX} STREQUAL "/usr/local") -- install(CODE "execute_process(COMMAND ${PYTHON_EXECUTABLE} ${openbabel_SOURCE_DIR}/scripts/python/setup.py install --prefix=${CMAKE_INSTALL_PREFIX} WORKING_DIRECTORY ${openbabel_BINARY_DIR}/scripts)") -+ install(CODE "execute_process(COMMAND ${PYTHON_EXECUTABLE} ${openbabel_SOURCE_DIR}/scripts/python/setup.py install --prefix=$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX} WORKING_DIRECTORY ${openbabel_BINARY_DIR}/scripts)") - endif (${CMAKE_INSTALL_PREFIX} STREQUAL "/usr/local") - endif (PYTHON_PREFIX) - -@@ -228,8 +229,8 @@ if (DO_PERL_BINDINGS) - DEPENDS ${openbabel_SOURCE_DIR}/scripts/perl/openbabel-perl.cpp +diff -up openbabel-2.3.1/scripts/CMakeLists.txt.r openbabel-2.3.1/scripts/CMakeLists.txt +--- openbabel-2.3.1/scripts/CMakeLists.txt.r 2011-10-08 22:09:17.000000000 +0200 ++++ openbabel-2.3.1/scripts/CMakeLists.txt 2011-10-12 18:57:31.000000000 +0200 +@@ -251,7 +251,7 @@ if (DO_PERL_BINDINGS) WORKING_DIRECTORY ${openbabel_BINARY_DIR}/scripts/perl ) -- add_dependencies(bindings_perl pre_bindings_perl) -- install(CODE "execute_process(COMMAND make install WORKING_DIRECTORY ${openbabel_BINARY_DIR}/scripts/perl)") -+ add_dependencies(bindings_perl pre_bindings_perl openbabel) -+ install(CODE "execute_process(COMMAND make install_vendor WORKING_DIRECTORY ${openbabel_BINARY_DIR}/scripts/perl)") - + add_dependencies(bindings_perl pre_bindings_perl openbabel) +- install(CODE "execute_process(COMMAND make install DESTDIR=\$ENV{DESTDIR} WORKING_DIRECTORY ${openbabel_BINARY_DIR}/scripts/perl)") ++ install(CODE "execute_process(COMMAND make install_vendor DESTDIR=\$ENV{DESTDIR} WORKING_DIRECTORY ${openbabel_BINARY_DIR}/scripts/perl)") + else (NOT MSVC) add_library(bindings_perl MODULE ${openbabel_SOURCE_DIR}/scripts/perl/openbabel-perl.cpp) -@@ -282,20 +283,20 @@ if (DO_RUBY_BINDINGS) - COMMAND ${CMAKE_COMMAND} -E make_directory ${openbabel_BINARY_DIR}/scripts/ruby - ) - add_custom_target(bindings_ruby ALL -- COMMAND ${RUBY_EXECUTABLE} ${openbabel_SOURCE_DIR}/scripts/ruby/extconf.rb --with-openbabel-lib=${BABEL_LIBRARY} --with-openbabel-include=${openbabel_BINARY_DIR}/include -+ COMMAND ${RUBY_EXECUTABLE} ${openbabel_SOURCE_DIR}/scripts/ruby/extconf.rb --with-openbabel-lib=${openbabel_BINARY_DIR}/lib${LIB_SUFFIX} --with-openbabel-include=${openbabel_BINARY_DIR}/include - COMMAND ${CMAKE_COMMAND} -E echo "Compiling Ruby bindings" - COMMAND make - DEPENDS ${openbabel_SOURCE_DIR}/scripts/ruby/openbabel-ruby.cpp - WORKING_DIRECTORY ${openbabel_BINARY_DIR}/scripts/ruby - ) -- add_dependencies(bindings_ruby pre_bindings_ruby) -+ add_dependencies(bindings_ruby pre_bindings_ruby openbabel) - if (RUBY_PREFIX) - install(CODE "execute_process(COMMAND DESTDIR=${RUBY_PREFIX} make install WORKING_DIRECTORY ${openbabel_BINARY_DIR}/scripts/ruby)") - else (RUBY_PREFIX) - if (${CMAKE_INSTALL_PREFIX} STREQUAL "/usr/local") - install(CODE "execute_process(COMMAND make install WORKING_DIRECTORY ${openbabel_BINARY_DIR}/scripts/ruby)") - else (${CMAKE_INSTALL_PREFIX} STREQUAL "/usr/local") -- install(CODE "execute_process(COMMAND DESTDIR=${CMAKE_INSTALL_PREFIX} make install WORKING_DIRECTORY ${openbabel_BINARY_DIR}/scripts/ruby)") -+ install(CODE "execute_process(COMMAND make DESTDIR=$ENV{DESTDIR} install WORKING_DIRECTORY ${openbabel_BINARY_DIR}/scripts/ruby)") - endif (${CMAKE_INSTALL_PREFIX} STREQUAL "/usr/local") - endif (RUBY_PREFIX) - else(NOT MSVC) -diff -up openbabel-2.3.0/scripts/perl/Makefile.PL.r openbabel-2.3.0/scripts/perl/Makefile.PL ---- openbabel-2.3.0/scripts/perl/Makefile.PL.r 2010-10-23 03:44:58.000000000 +0200 -+++ openbabel-2.3.0/scripts/perl/Makefile.PL 2010-11-24 22:53:46.417249628 +0100 -@@ -12,6 +12,9 @@ $cmakebindir = @ENV{"OBJ_DIR"}; - if (-e "$cmakebindir/lib/libopenbabel.so" || -e "$cmakebindir/lib/libopenbabel.dylib") { - check_lib_or_exit( lib => 'openbabel' , libpath => "$cmakebindir/lib"); - } -+elsif (-e "$cmakebindir/lib64/libopenbabel.so") { -+ check_lib_or_exit( lib => 'openbabel' , libpath => "$cmakebindir/lib64"); -+} - else { - check_lib_or_exit( lib => 'openbabel' , libpath => @ENV{"LD_LIBRARY_PATH"}); - } -@@ -21,6 +24,8 @@ $ldfrom = "\$(OBJECT) -L$cmakebindir/lib - if (-r "$cmakebindir/lib/libopenbabel.dylib") and (-s _) and (-B _); - $ldfrom = "\$(OBJECT) -L$cmakebindir/lib -lopenbabel" - if (-r "$cmakebindir/lib/libopenbabel.so") and (-s _) and (-B _); -+$ldfrom = "\$(OBJECT) -L$cmakebindir/lib64 -lopenbabel" -+ if (-r "$cmakebindir/lib64/libopenbabel.so") and (-s _) and (-B _); - - # See lib/ExtUtils/MakeMaker.pm for details of how to influence - # the contents of the Makefile that is written. -diff -up openbabel-2.3.0/scripts/python/setup.py.r openbabel-2.3.0/scripts/python/setup.py ---- openbabel-2.3.0/scripts/python/setup.py.r 2010-10-26 16:39:01.000000000 +0200 -+++ openbabel-2.3.0/scripts/python/setup.py 2010-11-23 01:56:55.083627521 +0100 -@@ -17,7 +17,9 @@ obExtension = Extension('_openbabel', - [os.path.join(srcdir, "openbabel-python.cpp")], - include_dirs=[os.path.join(srcdir, "..", "..", "include"), - os.path.join("..", "include")], -- library_dirs=[os.path.join("..", "lib")], -+ library_dirs=[os.path.join(srcdir, "..", "..", "lib"), -+ os.path.join(srcdir, "..", "..", "lib64"), -+ os.path.join("..", "lib")], - libraries=['openbabel'] - ) - diff --git a/openbabel.spec b/openbabel.spec index 5eccb6c..504b314 100644 --- a/openbabel.spec +++ b/openbabel.spec @@ -9,19 +9,16 @@ %define beta_dir %{nil} Name: openbabel -Version: 2.3.0 -Release: 5%{beta_ver}%{?dist} +Version: 2.3.1 +Release: 1%{beta_ver}%{?dist} Summary: Chemistry software file format converter License: GPLv2 Group: Applications/File URL: http://openbabel.org/ Source: http://downloads.sourceforge.net/sourceforge/openbabel/%{name}-%{version}%{beta_str}.tar.gz Patch1: %{name}-rpm.patch -Patch3: %{name}-inchi.patch # fix plugin directory location (#680292, patch by lg) Patch4: openbabel-2.3.0-plugindir.patch -# show forcefields list in obenergy output (#680292, patch by lg) -Patch5: openbabel-2.3.0-obenergy-fflist.patch BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n) BuildRequires: cmake BuildRequires: eigen2-devel @@ -122,9 +119,7 @@ Ruby wrapper for the Open Babel library. %prep %setup -q -n %{name}-%{version}%{beta_dir} %patch1 -p1 -b .r -%patch3 -p1 -b .inchi %patch4 -p1 -b .plugindir -%patch5 -p1 -b .obenergy-fflist chmod 644 src/formats/{fchk,genbank,mmcif}format.cpp chmod 644 src/math/align.cpp chmod 644 include/openbabel/{graphsym.h,math/align.h} @@ -145,7 +140,8 @@ make VERBOSE=1 %{?_smp_mflags} touch scripts/CMakeLists.txt make VERBOSE=1 DESTDIR=$RPM_BUILD_ROOT install -rm $RPM_BUILD_ROOT%{perl_archlib}/perllocal.pod +rm $RPM_BUILD_ROOT%{_libdir}/cmake/openbabel2/*.cmake +rm $RPM_BUILD_ROOT%{_libdir}/perl5/perllocal.pod rm -f $RPM_BUILD_ROOT%{perl_vendorarch}/auto/Chemistry/OpenBabel/{.packlist,OpenBabel.bs} chmod 755 $RPM_BUILD_ROOT%{perl_vendorarch}/auto/Chemistry/OpenBabel/OpenBabel.so @@ -170,7 +166,7 @@ chmod 755 $RPM_BUILD_ROOT%{perl_vendorarch}/auto/Chemistry/OpenBabel/OpenBabel.s %files gui %defattr(-,root,root,-) -%{_bindir}/OBGUI +%{_bindir}/obgui %files libs %defattr(-,root,root,-) @@ -205,6 +201,10 @@ chmod 755 $RPM_BUILD_ROOT%{perl_vendorarch}/auto/Chemistry/OpenBabel/OpenBabel.s %{ruby_sitearch}/openbabel.so %changelog +* Fri Oct 21 2011 Dominik Mierzejewski 2.3.0-1 +- update to 2.3.1 +- drop obsolete patches (merged upstream) + * Mon Jun 20 2011 Marcela Mašláňová - 2.3.0-5 - Perl mass rebuild diff --git a/sources b/sources index 351778d..c6b55a2 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -effda01ed4a31d18d8e3d08191799608 openbabel-2.3.0.tar.gz +1f029b0add12a3b55582dc2c832b04f8 openbabel-2.3.1.tar.gz